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[PRE REVIEW]: Mashpit: sketching out genomic epidemiology #4437

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@lskatz<!--end-author-handle-- (Lee Katz) Repository: https://github.com/tongzhouxu/mashpit Branch with paper.md (empty if default branch): master Version: v0.9.2 Editor: Pending Reviewers: Pending Managing EiC: Arfon Smith

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Author instructions

Thanks for submitting your paper to JOSS @lskatz. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @luizirber.

@lskatz if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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editorialbot commented 2 years ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 2 years ago
Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (502.7 files/s, 34938.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            102             82            579
Markdown                         2             49              0            193
TeX                              1              9              0             81
YAML                             1              0              0             16
Standard ML                      1              0              0              1
-------------------------------------------------------------------------------
SUM:                            16            160             82            870
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1003

editorialbot commented 2 years ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.00027 is OK

MISSING DOIs

- 10.1093/bioinformatics/bty407 may be a valid DOI for title: Nextstrain: real-time tracking of pathogen evolution
- 10.2807/1560-7917.es.2017.22.23.30544 may be a valid DOI for title: PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance
- 10.3389/fmicb.2017.00375 may be a valid DOI for title: A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens

INVALID DOIs

- None
editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 2 years ago

@editorialbot query scope

@lskatz – due to the small size of this code, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. We should get back to you sometime next week.

editorialbot commented 2 years ago

Submission flagged for editorial review.

danielskatz commented 2 years ago

👋 @lskatz - I'm sorry to say that after discussion amongst the JOSS editors, we have decided that this submission does not meet the substantial scholarly effort criterion for review by JOSS. Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your work.

danielskatz commented 2 years ago

@editorialbot reject

editorialbot commented 2 years ago

Paper rejected.

lskatz commented 2 years ago

Thank you for your consideration @danielskatz @arfon @luizirber. We strongly believe that this is crucial software for genomic epidemiology and therefore adds value to public health, but at the same time we want to respect the integrity of the journal. We will continue to work on this software. If we substantially add onto the software and add use-cases to the documentation to reflect its importance, could it be reconsidered for submission to JOSS?

danielskatz commented 2 years ago

Yes, certainly. We are trying to balance publishing on useful software and being seen as publishing substantial work similar in effort to other journals, which is sometimes tricky.